[Insight-users] Fwd: imageregistration with mask fails because of all points outside of all points mapped outside of moving image

[michiel mentink]

Dear Luis,

Background: I have an image volume, MRI of the knee. The tibia is segmented
and
all the 'femur' voxels have grey values (not binary). All the rest is black.
Therefore, I create a mask by applying a thresholder with a threshold of 1:
all the
voxels that have intensity>0 are given the value '1'.

    typedef itk::ThresholdImageFilter< FixedImageType > ThresholdFilterType;
    ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New();
    thresholder->SetInput( fixedImage);
    thresholder->SetOutsideValue( 1 );
    thresholder->ThresholdAbove( 0 );
    thresholder->Update();

  // insert caster here, casting from float to unsigned char
  typedef  unsigned char  MaskPixelType;
  typedef itk::Image< MaskPixelType, Dimension > MaskImageType;
  typedef itk::CastImageFilter< FixedImageType, MaskImageType >
CastFilterType;

  CastFilterType::Pointer  caster =  CastFilterType::New();
  caster->SetInput( thresholder->GetOutput() );

  // create a 3D mask type
  typedef itk::ImageMaskSpatialObject< 3 >   MaskType;
  // then create the mask itself
  MaskType::Pointer  mask = MaskType::New();

  //connect the binary image to the mask
  mask->SetImage(caster->GetOutput() );

  // pass the spatial object mask to the image metric
  metric->SetFixedImageMask( mask);
//  metric->SetMovingImageMask( mask);

  // write the mask to a file, just to check if thresholding went alright
  typedef itk::ImageFileWriter< MaskImageType >  MaskImageWriter;
  MaskImageWriter::Pointer writerBinary = MaskImageWriter::New();
  writerBinary->SetInput( caster->GetOutput() );
  writerBinary->SetFileName("mask.mhd" );
  writerBinary->Update();
  std::cout << "mask created" << std::endl << std::endl;

I'm afraid I can't post the mask file to the mailing list (1.7MB) but I'll
mail it to you.

cheers,

Michael




On Sat, Mar 6, 2010 at 11:02 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:

> Hi Michiel,
>
> Thanks for sharing your findings in this problem.
>
> Can you tell us more about the mask (the segmentation)
> that you created ?
>
> Have you checked this mask with any visualization
> application ?
>
> What are the pixel values ?
>
> Is there a chance that you could share that binary image
> with us ?
>
>
>    Thanks
>
>
>          Luis
>
> ---------------------------------------------------------------------------
> On Fri, Mar 5, 2010 at 11:28 AM, michiel mentink
> <michael.mentink at st-hughs.ox.ac.uk> wrote:
> > Dear all,
> >
> > When running an image registration algorithm with mask, I get this error:
> >
> > File:
> > /MMprogs/src/ITK_src/Code/Algorithms/itkMeanSquaresImageToImageMetric.txx
> > Line: 364
> > Description: itk::ERROR: MeanSquaresImageToImageMetric(0x95f63f0): All
> the
> > points mapped to outside of the moving image
> >
> > I've traced this to the following problem:
> > in ImageMaskSpatialObject->IsInside(), all points are found outside of
> the
> > mask/image (?)
> >
> > and this is because the boundingbox of the mask has bounding values of 0,
> 0,
> > 0, 0, 0, 0, so indeed, there are no points that
> > can be found inside these values.
> >
> > I am a bit stuck now, apparently, the mask that I created from a
> segmented
> > volume is not converted into a bounding box correctly.
> >
> > Where do I check to find out why this is happening?
> >
> > cheers,
> >
> > Michael
> >
> >
> > ps: some more info about my data:
> >
> > new moving image origin:    [0, 0, 0]
> > fixed image size:      [215, 172, 48]
> > fixed image origin:    [44.0625, 0, 0]
> > fixed image spacing:   [0.3125, 0.3125, 1.9808]
> > fixed image direction:
> > 1 0 0
> > 0 1 0
> > 0 0 1
> >
> >
> > moving image size:      [512, 512, 52]
> > moving image origin:    [0, 0, 0]
> > moving image spacing:   [0.3125, 0.3125, 1.92911]
> > moving image direction:
> > 1 0 0
> > 0 1 0
> > 0 0 1
> >
> >
> > image mask size:      [215, 172, 48]
> > image mask origin:    [44.0625, 0, 0]
> > image mask spacing:   [0.3125, 0.3125, 1.9808]
> > image mask direction:
> > 1 0 0
> > 0 1 0
> > 0 0 1
> >
> >
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